+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import static org.testng.AssertJUnit.assertNotNull;
+
+import jalview.api.AlignExportSettingI;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
-import org.junit.After;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
public class JSONFileTest
{
- private JSONFile jsonFile;
private int TEST_SEQ_HEIGHT = 0;
private int TEST_GRP_HEIGHT = 0;
- @Before
- public void setUp() throws Exception
- {
- jsonFile = new JSONFile();
+ private int TEST_ANOT_HEIGHT = 0;
+
+ private int TEST_CS_HEIGHT = 0;
+
+ private String TEST_JSON_FILE = "examples/example.json";
+
+ private Alignment alignment;
+
+ private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();
+
+ private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();
+
+ private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
+
+ private ColumnSelection expectedColSel = new ColumnSelection();
+
+ private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
+
+ private AlignmentI testAlignment;
+
+ private int passedCount;
+
+ private JSONFile testJsonFile;
+
+ private JSONFile jf;
+ @BeforeTest(alwaysRun = true)
+ public void setup() throws Exception
+ {
// create and add sequences
Sequence[] seqs = new Sequence[5];
seqs[0] = new Sequence("FER_CAPAN",
seqs[4] = new Sequence("Q7XA98_TRIPR",
"ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39);
+ SequenceI hiddenSeq = new Sequence("FER_TOCH",
+ "FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF", 3, 34);
+ expectedHiddenSeqs[0] = hiddenSeq;
+
// create and add sequence features
SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
- "desciption", "status", 22, 29, "jalview");
+ "desciption", "status", 6, 15, "Jalview");
SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
- "desciption", "status", 25, 32, "jalview");
+ "desciption", "status", 9, 18, "Jalview");
SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
- "desciption", "status", 25, 32, "jalview");
+ "desciption", "status", 9, 18, "Jalview");
seqs[2].addSequenceFeature(seqFeature2);
seqs[3].addSequenceFeature(seqFeature3);
seqs[4].addSequenceFeature(seqFeature4);
- // add created features to features displayed
- FeaturesDisplayed fDis = new FeaturesDisplayed();
- fDis.setVisible("feature_x");
- jsonFile.setDisplayedFeatures(fDis);
- JSONFile.setSeqFeaturesEnabled(true);
-
for (Sequence seq : seqs)
{
seq.setDatasetSequence(seq);
- jsonFile.seqs.add(seq);
+ expectedSeqs.put(seq.getName(), seq);
}
// create and add sequence groups
ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
- grpSeqs.add(seqs[0]);
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
- ColourSchemeI scheme = jsonFile.getJalviewColorScheme("zappo");
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1114606272",
- scheme, true, true, false, 2, 9);
+ grpSeqs.add(seqs[3]);
+ grpSeqs.add(seqs[4]);
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
+ null, true, true, false, 21, 29);
+ ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+ "zappo", seqGrp);
+ seqGrp.cs = scheme;
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
- jsonFile.seqGroups.add(seqGrp);
+
+ expectedGrps.put(seqGrp.getName(), seqGrp);
// create and add annotation
Annotation[] annot = new Annotation[35];
annot[2] = new Annotation("α", "", 'H', 0);
annot[3] = new Annotation("α", "", 'H', 0);
annot[4] = new Annotation("α", "", 'H', 0);
- annot[5] = new Annotation("α", "", 'H', 0);
+ annot[5] = new Annotation("", "", '\u0000', 0);
annot[6] = new Annotation("", "", '\u0000', 0);
annot[7] = new Annotation("", "", '\u0000', 0);
- annot[8] = new Annotation("", "", '\u0000', 0);
- annot[9] = new Annotation("", "", '\u0000', 0);
+ annot[8] = new Annotation("β", "", 'E', 0);
+ annot[9] = new Annotation("β", "", 'E', 0);
annot[10] = new Annotation("β", "", 'E', 0);
annot[11] = new Annotation("β", "", 'E', 0);
- annot[12] = new Annotation("", "", '\u0000', 0);
- annot[13] = new Annotation("", "", '\u0000', 0);
- annot[14] = new Annotation("", "", '\u0000', 0);
- annot[15] = new Annotation("", "", '\u0000', 0);
- annot[16] = new Annotation("α", "", 'H', 0);
- annot[17] = new Annotation("α", "", 'H', 0);
- annot[18] = new Annotation("α", "", 'H', 0);
- annot[19] = new Annotation("α", "", 'H', 0);
- annot[20] = new Annotation("α", "", 'H', 0);
-
+ annot[12] = new Annotation("β", "", 'E', 0);
+ annot[13] = new Annotation("β", "", 'E', 0);
+ annot[14] = new Annotation("β", "", 'E', 0);
+ annot[15] = new Annotation("β", "", 'E', 0);
+ annot[16] = new Annotation("", "", '\u0000', 0);
+ annot[17] = new Annotation("", "", '\u0000', 0);
+ annot[18] = new Annotation("", "", '\u0000', 0);
+ annot[19] = new Annotation("", "", '\u0000', 0);
+ annot[20] = new Annotation("", "", '\u0000', 0);
annot[21] = new Annotation("", "", '\u0000', 0);
annot[22] = new Annotation("", "", '\u0000', 0);
annot[23] = new Annotation("", "", '\u0000', 0);
annot[24] = new Annotation("", "", '\u0000', 0);
annot[25] = new Annotation("", "", '\u0000', 0);
- annot[26] = new Annotation("", "", '\u0000', 0);
- annot[27] = new Annotation("", "", '\u0000', 0);
- annot[28] = new Annotation("", "", '\u0000', 0);
- annot[29] = new Annotation("", "", '\u0000', 0);
- annot[30] = new Annotation("", "", '\u0000', 0);
+ annot[26] = new Annotation("α", "", 'H', 0);
+ annot[27] = new Annotation("α", "", 'H', 0);
+ annot[28] = new Annotation("α", "", 'H', 0);
+ annot[29] = new Annotation("α", "", 'H', 0);
+ annot[30] = new Annotation("α", "", 'H', 0);
annot[31] = new Annotation("", "", '\u0000', 0);
- annot[32] = new Annotation("β", "", 'E', 0);
- annot[33] = new Annotation("β", "", 'E', 0);
- annot[34] = new Annotation("β", "", 'E', 0);
+ annot[32] = new Annotation("", "", '\u0000', 0);
+ annot[33] = new Annotation("", "", '\u0000', 0);
+ annot[34] = new Annotation("", "", '\u0000', 0);
AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
"Secondary Structure", "New description", annot);
- jsonFile.annotations.add(alignAnnot);
+ expectedAnnots.put(alignAnnot.label, alignAnnot);
+
+ expectedColSel.hideColumns(32, 33);
+ expectedColSel.hideColumns(34, 34);
+
+ TEST_SEQ_HEIGHT = expectedSeqs.size();
+ TEST_GRP_HEIGHT = expectedGrps.size();
+ TEST_ANOT_HEIGHT = expectedAnnots.size();
+ TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
+
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
+
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
+ try
+ {
+ alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
+ jf = (JSONFile) formatAdapter.getAlignFile();
+
+ AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
+ jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
+ af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
+
+ formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+ String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
+ af.alignPanel.getAlignment(), false);
+
+ formatAdapter = new AppletFormatAdapter();
+ testAlignment = formatAdapter.readFile(jsonOutput,
+ AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
+ testJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ // System.out.println(jsonOutput);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ }
- // Alignment al = new Alignment(seqs);
- TEST_SEQ_HEIGHT = jsonFile.seqs.size();
- TEST_GRP_HEIGHT = jsonFile.seqGroups.size();
+ @BeforeMethod(alwaysRun = true)
+ public void methodSetup()
+ {
+ passedCount = 0;
}
- @After
+ @AfterTest
public void tearDown() throws Exception
{
+ testJsonFile = null;
+ alignment = null;
+ expectedSeqs = null;
+ expectedAnnots = null;
+ expectedGrps = null;
+ testAlignment = null;
+ jf = null;
}
- @Test
- public void test()
+ @Test(groups = { "Functional" })
+ public void roundTripTest()
{
- String jsonOuput = jsonFile.print();
- // System.out.println(">>>>>>>>>>>>>> " + jsonOuput);
- JSONFile output = new JSONFile().parse(jsonOuput);
+ assertNotNull("JSON roundtrip test failed!", testJsonFile);
+ }
- int matchedCounter = 0;
- for (SequenceI in : jsonFile.getSeqs())
+ @Test(groups = { "Functional" })
+ public void testSeqParsed()
+ {
+ assertNotNull("Couldn't read supplied alignment data.", testAlignment);
+ Assert.assertNotNull(testAlignment.getSequences());
+ for (SequenceI seq : testAlignment.getSequences())
{
- for (SequenceI out : output.getSeqs())
- {
- if (in.getName().equals(out.getName())
- && in.getSequenceAsString().equals(
- out.getSequenceAsString())
- && in.getStart() == out.getStart()
- && in.getEnd() == out.getEnd() && featuresMatched(in, out))
- {
- // System.out.println(">>>> Seq Match Detected");
- ++matchedCounter;
- }
- }
+ SequenceI expectedSeq = expectedSeqs.get(seq.getName());
+ AssertJUnit.assertTrue(
+ "Failed Sequence Test for >>> " + seq.getName(),
+ isSeqMatched(expectedSeq, seq));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some Sequences did not pass the test",
+ TEST_SEQ_HEIGHT, passedCount);
+ }
+
+ @Test(groups = { "Functional" })
+ public void hiddenColsTest()
+ {
+ ColumnSelection cs = testJsonFile.getColumnSelection();
+ Assert.assertNotNull(cs);
+ Assert.assertNotNull(cs.getHiddenColumns());
+ List<int[]> hiddenCols = cs.getHiddenColumns();
+ Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
+ Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(),
+ "Mismatched hidden columns!");
+ }
+
+ @Test(groups = { "Functional" })
+ public void hiddenSeqsTest()
+ {
+ Assert.assertNotNull(testJsonFile.getHiddenSequences(),
+ "Hidden sequence Expected but found Null");
+ Assert.assertEquals(jf.getHiddenSequences().length, 1, "Hidden sequece");
+ }
+
+ @Test(groups = { "Functional" })
+ public void colorSchemeTest()
+ {
+ Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
+ "Colourscheme is null, parsing failed!");
+ Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
+ "Zappo colour scheme expected!");
+ }
+
+ @Test(groups = { "Functional" })
+ public void isShowSeqFeaturesSet()
+ {
+ Assert.assertTrue(testJsonFile.isShowSeqFeatures(),
+ "Sequence feature isDisplayed setting expected to be true");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGrpParsed()
+ {
+ Assert.assertNotNull(testAlignment.getGroups());
+ for (SequenceGroup seqGrp : testAlignment.getGroups())
+ {
+ SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
+ AssertJUnit.assertTrue(
+ "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
+ isGroupMatched(expectedGrp, seqGrp));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
+ TEST_GRP_HEIGHT, passedCount);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAnnotationParsed()
+ {
+ Assert.assertNotNull(testAlignment.getAlignmentAnnotation());
+ for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation())
+ {
+ AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label);
+ AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ + annot.label, isAnnotationMatched(expectedAnnot, annot));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some Sequences did not pass the test",
+ TEST_ANOT_HEIGHT, passedCount);
+ }
+
+ public boolean isAnnotationMatched(AlignmentAnnotation eAnnot,
+ AlignmentAnnotation annot)
+ {
+ if (!eAnnot.label.equals(annot.label)
+ || !eAnnot.description.equals(annot.description)
+ || eAnnot.annotations.length != annot.annotations.length)
+ {
+ return false;
}
- Assert.assertTrue(matchedCounter == TEST_SEQ_HEIGHT);
- matchedCounter = 0;
- for (SequenceGroup in : jsonFile.getSeqGroups())
+ for (int x = 0; x < annot.annotations.length; x++)
{
- for (SequenceGroup out : output.getSeqGroups())
+ Annotation y = annot.annotations[x];
+ Annotation z = annot.annotations[x];
+
+ if (!y.displayCharacter.equals(z.displayCharacter)
+ || y.value != z.value
+ || y.secondaryStructure != z.secondaryStructure)
{
- if (in.getName().equals(out.getName())
- && in.getColourText() == out.getColourText()
- && in.getDisplayBoxes() == out.getDisplayBoxes()
- && in.getIgnoreGapsConsensus() == out
- .getIgnoreGapsConsensus() && in.cs.equals(out.cs)
- && in.getSequences().size() == out.getSequences().size())
- {
- // System.out.println(">>>> Grp Match Detected");
- ++matchedCounter;
- }
+ return false;
}
- Assert.assertTrue(matchedCounter == TEST_GRP_HEIGHT);
}
+ return true;
+ }
+
+ public boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
+ {
+ System.out.println("Testing >>> " + actualSeq.getName());
+ if (expectedSeq.getName().equals(actualSeq.getName())
+ && expectedSeq.getSequenceAsString().equals(
+ actualSeq.getSequenceAsString())
+ && expectedSeq.getStart() == actualSeq.getStart()
+ && expectedSeq.getEnd() == actualSeq.getEnd()
+ && featuresMatched(expectedSeq, actualSeq))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public boolean isGroupMatched(SequenceGroup expectedGrp,
+ SequenceGroup actualGrp)
+ {
+
+ System.out.println("Testing >>> " + actualGrp.getName());
+ System.out.println(expectedGrp.getName() + " | " + actualGrp.getName());
+ System.out.println(expectedGrp.getColourText() + " | "
+ + actualGrp.getColourText());
+ System.out.println(expectedGrp.getDisplayBoxes() + " | "
+ + actualGrp.getDisplayBoxes());
+ System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
+ + actualGrp.getIgnoreGapsConsensus());
+ System.out.println(expectedGrp.getSequences().size() + " | "
+ + actualGrp.getSequences().size());
+ System.out.println(expectedGrp.getStartRes() + " | "
+ + actualGrp.getStartRes());
+ System.out.println(expectedGrp.getEndRes() + " | "
+ + actualGrp.getEndRes());
+ System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
+
+ if (expectedGrp.getName().equals(actualGrp.getName())
+ && expectedGrp.getColourText() == actualGrp.getColourText()
+ && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
+ && expectedGrp.getIgnoreGapsConsensus() == actualGrp
+ .getIgnoreGapsConsensus()
+ && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
+ && expectedGrp.getSequences().size() == actualGrp
+ .getSequences().size()
+ && expectedGrp.getStartRes() == actualGrp.getStartRes()
+ && expectedGrp.getEndRes() == actualGrp.getEndRes())
+ {
+ return true;
+ }
+ return false;
}
private boolean featuresMatched(SequenceI seq1, SequenceI seq2)
int testSize = inFeature.length;
int matchedCount = 0;
- // System.out.println(">>>>>>>>>>>>> 1");
for (SequenceFeature in : inFeature)
{
- for (SequenceFeature out : inFeature)
+ for (SequenceFeature out : outFeature)
{
+ System.out.println(out.getType() + " | " + in.getType());
+ System.out.println(out.getBegin() + " | " + in.getBegin());
+ System.out.println(out.getEnd() + " | " + in.getEnd());
+
if (inFeature.length == outFeature.length
&& in.getBegin() == out.getBegin()
&& in.getEnd() == out.getEnd()
&& in.getScore() == out.getScore()
- && in.getFeatureGroup().equals(out.getFeatureGroup()))
+ && in.getFeatureGroup().equals(out.getFeatureGroup())
+ && in.getType().equals(out.getType()))
{
++matchedCount;
}
}
}
+ System.out.println("matched count >>>>>> " + matchedCount);
if (testSize == matchedCount)
{
matched = true;
git://source.jalview.org / jalview.git / blobdiff